Antigen

Antigen Class

TFs and others

Antigen

Lmnb1

Cell type

Cell type Class

Neural

Cell type

Hippocampus

MeSH Description

A curved elevation of GRAY MATTER extending the entire length of the floor of the TEMPORAL HORN of the LATERAL VENTRICLE (see also TEMPORAL LOBE). The hippocampus proper, subiculum, and DENTATE GYRUS constitute the hippocampal formation. Sometimes authors include the ENTORHINAL CORTEX in the hippocampal formation.

Sample

source_name

Mice hippocampus

strain

CBA x C57BL/6 (50% CBA & 50% C57BL6)

genotype/variation

WT

tissue

hippocampal tissue

age

30-week-old mice

chip antibody

Rabbit anti-Lamin B1 polyclonal antibody, Abcam, Cat# ab16048

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP-seq: Frozen hippocampus from 5 mice were pooled together, homogenized in PBS supplemented with proteinase inhibitors and posteriorly cross-linked with formaldehyde 1% for 15 minutes at r. t. Cross-linking reaction was stopped by a 5 minutes incubation with 2 M glycine and the cross-linked material was washed 3 times with ice-cold PBS. Cells were lysed and nuclei were extracted using nuclei extraction buffer. Purified nuclear fraction was subjected to sonication using Bioruptor Pico (Diagenode) to obtain DNA fragments of 200-500 bp. Sonicated chromatin was incubated with anti-rabbit magnetic bead pre-complexed with 10 µg of α-lamin B1 antibody O/N at 4 ºC. After 6 washes with RIPA buffer, chromatin was eluted and de-crosslinked by O/N incubation at 65 ºC, followed by a 30 minutes RNAse and 2 hours Proteinase K treatments. DNA purification was carried out with MinElute PCR Purification KIT and libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit from Illumina according to the manufacturer's instructions. DNA size selection was performed after PCR amplification using E-Gel Precast Agarose Electrophoresis System. Samples were sequenced single-end using 50 bp reads on the Hi-Seq 4000 platforms. For each biological replicate (R1, R2 and R3), three samples corresponding to their respective sequencing lane are provided. Libraries were prepared according to Illumina instructions.

Sequencing Platform

instrument_model

Illumina HiSeq 4000

mm10

Number of total reads

25008599

Reads aligned (%)

90.6

Duplicates removed (%)

33.2

Number of peaks

435 (qval < 1E-05)

mm9

Number of total reads

25008599

Reads aligned (%)

90.4

Duplicates removed (%)

33.3

Number of peaks

461 (qval < 1E-05)